This repository hosts the User Interface for NetPyNE. NetPyNE is a python package to facilitate the development, parallel simulation and analysis of biological neuronal networks using the NEURON simulator.
Install NetPyNE User Interface
Select one option to install the NetPyNE User Interface.
If you are familiar with NEURON and have already NEURON installed in your machine you can proceed using Pip. If you want a container which comes with everything preinstalled including NEURON you can use the Docker image. Using docker you will still be able to mount a local folder which will be your NetPyNE workspace. If you don't have docker installed in your system and you have had troubles installing it you can opt for the Virtual Machine installation.
Install NetPyNE User Interface from sources (for developers)
Python Dependencies
We recommend the use of a new python 3 virtual environment:
python3 -m venv npenv
source npenv/bin/activateOr, with conda
conda create -n netpyne python=3.7
conda activate netpyneRun install script
python utilities/install.pyStart application
./NetPyNE-UIFor debugging you can use run.py instead
python run.pyRun NetPyNE User Interface in Docker
Ensure that you have Docker installed on your system.
Build the image
docker build -t netpyne-uiRun the image
docker run -p 8888:8888 netpyne-ui End-to-end tests
End-to-end tests are located in tests/deployment/frontend/e2e.
Ensure that the application is running in a blank state, since end-to-end tests interact with the running application.
Install packages
cd tests/frontend/e2e
npm installStart tests
npm run testContainerized tests
You can also use docker-compose to run the tests.
Ensure that you have Docker installed on your system.
Build the images
cd tests/deployment
sh build.shRun the tests
docker-compose up --abort-on-container-exit --exit-code-from netpyne-ui-e2eAdditional Notes
NetPyNE-UI is being developed in collaboration with the Neurosim Lab. See the Wiki for more info!